In MLB,the vast majority of attempts at a squeeze will come when the defense is not paying attention (beyond simply not bringing the infield in). We don't have the ability to look onto a field, see that the 3B is not thinking bunt, and signal for a squeeze. I agree that RL teams will almost always guard against a squeeze, but they can do it by having the CIF take one or two steps in, to show the offense that they're guarding against the bunt. A good bunter might still be asked to squeeze, but David Ortiz and Adam Dunn aren't going to try it.
I believe the same is true on Hold's effect. People get steamed when a speedster is thrown out when the defense does not use Hold. Leaving Hold off is not the same as fielder's indifference, and I long ago realized that Hold has little or no effect on steals, but does affect taking extra bases and double plays. That's why Sparky ALWAYS uses Hold with a runner at 2nd (to reduce the scoring chances on a single), but not always with a runner at first. Similarly on bunts, not bringing the infield in is different from playing it deep (which we do not have the ability to do) and inviting a bunt.
But to me, the biggest issue is the completely unrealistic certainty that the runner at third will go home on a bunt, regardless of H&R of IF IN. It is a programming flaw that takes away the ability to bunt to avoid a 1st-and-3rd DP without the run scoring. Too bad support didn't fix it while there they still had programmers. In short, they forgot to program in a safety squeeze.